When exporting a VGPS to GPX we get the option to refresh cache notes. I assume this parses cache notes for corrected coordinates. However I find it difficult understanding which option I need to choose for a given situation.

What actually does Refresh caches notes (fast) do? Why is it that Refresh cache notes (multis and puzzles) takes longer, yet is a subset of all caches in the query?

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If I understand it right, the API does provide PGC to filter (and download) only caches with User Notes. This means that really only the minimal amount of caches that you might have modified note for will get refreshed. The other option (multis and puzzles) means that all the Multi and Mystery caches will have to be downloaded, which is usually more caches than the previous option and will probably take more time.

Basically, there are two different fields that you as a (premium) user can add to a given cache listing:

Corrected Coordinates

Personal cache note

The main difference is that Corrected coordinate is semantically a new coordinate for the cache in question. The cache note, however, can be any text.

The main difference (as Jakuje points out) is that there is a an API call that Project-GC can make that fetches a list of all the caches that a given user has cache notes added to. A similar API call for corrected coordinates does (still) not exist.

Think of API calls as forms of questions you are allowed to ask. For instance, you are allowed to ask "Which caches does user X have notes on?". On coordinates, you are only allowed to ask "Does user X have corrected coordinates for cache Y?". Since you don't know in advance X and Y, it it practically impossible to fetch the answer ahead of time. Only when you provide a list of caches (f.x. in VGPS) Project-GC can iterate over them and ask the question for each one. This takes a lot of time and can not be done with any reasonable complexity in advance. Personal cache notes on the other hand can be easily fetched using the list utility and thus done efficiently.